Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using analytical theory and particle-based simulations. A reaction rate equation based on only these two processes turned out to be inconsistent with simulation results. However, accounting for diffusion inhibition by the surfaces of nearby obstacles, which affects access to reactants, it led to perfect agreement for reactions near impermeable planar membranes and improved agreement for reactions in crowded spaces. A separate model that quantified reactant occlusion by crowders, and extensions to a thermodynamic 'cavity' model proposed by Berezhkovskii and Szabo [25], were comparably successful. These results help elucidate reaction dynamics in confined spaces and improve prediction of in vivo reaction rates from in vitro ones.

中文翻译：

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表面和大分子拥挤对双分子反应速率的影响。

生物细胞是复杂的环境，充满大分子并被膜细分，这两种环境都会影响化学反应的速率。众所周知，拥挤减小了反应物可利用的体积，这增加了反应速率，并且还抑制了反应物扩散，从而降低了反应速率。这项工作使用分析理论和基于粒子的模拟对这些影响进行了定量研究。结果表明，仅基于这两个过程的反应速率方程与模拟结果不一致。但是，考虑到附近障碍物表面的扩散抑制作用会影响到反应物的进入，它导致了不可渗透平面膜附近反应的完美一致性，并改善了拥挤空间中反应的一致性。一个单独的模型来量化拥挤物对反应物的阻塞，以及Berezhkovskii和Szabo [25]提出的热力学“腔”模型的扩展，都取得了相当的成功。这些结果有助于阐明密闭空间中的反应动力学，并提高对体外反应速率的体内预测。